An in-house real-time polymerase chain reaction: standardisation and comparison with the Cobas Amplicor HBV monitor and Cobas AmpliPrep/Cobas TaqMan HBV tests for the quantification of hepatitis B virus DNA

This study aimed to standardise an in-house real-time polymerase chain reaction (rtPCR) to allow quantification of hepatitis B virus (HBV) DNA in serum or plasma samples, and to compare this method with two commercial assays, the Cobas Amplicor HBV monitor and the Cobas AmpliPrep/Cobas TaqMan HBV test. Samples from 397 patients from the state of São Paulo were analysed by all three methods. Fifty-two samples were from patients who were human immunodeficiency virus and hepatitis C virus positive, but HBV negative. Genotypes were characterised, and the viral load was measure in each sample. The in-house rtPCR showed an excellent success rate compared with commercial tests; inter-assay and intra-assay coefficients correlated with commercial tests (r = 0.96 and r = 0.913, p < 0.001) and the in-house test showed no genotype-dependent differences in detection and quantification rates. The in-house assay tested in this study could be used for screening and quantifying HBV DNA in order to monitor patients during therapy.

Checklist das Cryptophyceae do estado de São Paulo, Brasil

Usando como base de informações a monografia sobre o grupo publicada pelo projeto Flora Ficológica do Estado de São Paulo (Programa BIOTA), o acervo depositado no Herbário Científico do Estado de São Paulo Maria Eneyda P. Kauffmann Fidalgo (SP), a Lista de Espécies da Flora do Brasil e artigos científicos, dissertações e teses (com descrições e ilustrações) temos: nove gêneros e 39 espécies de criptoficeas, sendo 16 espécies exclusivas para o Estado de São Paulo, todas registradas em ambientes de água doce. A carência de especialistas no Estado de São Paulo e no Brasil, além de problemas de estratégia amostral, necessidade de uso da microscopia eletrônica e ausência de estudos de biologia molecular, são fatores que devem ter subestimado o conhecimento taxonômico de Cryptophyceae no Estado.

CORREDORES ECOLÓGICOS DA MATA ATLÂNTICA: VISÃO INTEGRADORA DO PLANEJAMENTO TERRITORIAL NO CONTÍNUO DE PARANAPIACABA -ESTADO DE SÃO PAULO - BRASIL

La visión bioregional de la conservación es reciente en Brasil. El planeamiento de mosaicos de las áreas protegidas con las intervenciones previstas en la zona tapón es un alternativa para corregir los dibujos actuales de áreas de protección. Lo Continuum Ecológico de Paranapicaba en el estado de Sâo Paulo (Brasil) se puede considerar uno de los corredores restantes más importantes de Mata Atlântica, reducidos hoy solamente a 7.3% de su extensión original. El Continuum Ecológico de Paranapiacaba tiene un alto nivel de biodiversidad. Se caracteriza por la vegetación que presenta gran diversidad estructural, y por lo tanto, así como  la presencia de  las  especie-llaves  endémicas, que  requieren  los  esfuerzos  efcientes para su conservación. Las estrategias que vienen siendo adoptados por  los parceiros de  la conservación buscan demostrar que es posible construir las ofertas adecuadas del uso y de la exploración sostenible de los recursos naturales. El empalme de algunas iniciativas socioambientales con el mosaico de las unidades de conservación, busca una “buena vecindad” a las unidades de la conservación que se hallan en el área-núcleo del Continuum. Palabras clave: Mata Atlântica, bosque lluvioso, buffer zone, conservación, áreas protegidas Abstract The bioregional vision of the conservation is recent in Brazil. The planning of mosaics of areas protected with interventions planned in the buffer zone is an alternative to correct the current drawings of Protecting Areas. The ecological Continuum of Paranapicaba in  the State of São Paulo  (Brazil) can be considered one of  the most  important  remaining corridors of Atlantic Rainforest, today reduced only 7.3% of its original extension. High level of biodiversity  is characterized by forest vegetation  that presents great structural diversity, and consequently, as well as presence of endemic species-keys, that require effcient efforts for its conservation. The strategies that come being adopted for partners of the conservation search to demonstrate that it is possible to construct to adequate proposals of use and sustainable exploration of the natural resources. The joint of the some social-environmental initiatives with the mosaic of Units of Conservation, searchs to construct a “good neighborhood” to the Units of Conservation that if fnd in the area-nucleus of Continuum.Key words: Mata Atlântica, rainforest, buffer zone, conservation, áreas protegidas

Assessment of heavy metals in soils of a vineyard region with the use of principal component analysis.

Agricultural management with chemicals may contaminate the soil with heavy metals. The objective of this study was to apply Principal Component Analysis and geoprocessing techniques to identify the origin of the metals Cu, Fe, Mn, Zn, Ni, Pb, Cr and Cd as potential contaminants of agricultural soils. The study was developed in an area of vineyard cultivation in the State of São Paulo, Brazil. Soil samples were collected and GPS located under different uses and coverings. The metal concentrations in the soils were determined using the DTPA method. The Cu and Zn content was considered high in most of the samples, and was larger in the areas cultivated with vineyards that had been under the application of fungicides for several decades. The concentrations of Cu and Zn were correlated. The geoprocessing techniques and the Principal Component Analysis confirmed the enrichment of the soil with Cu and Zn because of the use and management of the vineyards with chemicals in the preceding decades.

Seroprevalence of and risk factors for Toxoplasma gondii in sheep raised in the Jaboticabal microregion, São Paulo State, Brazil

Seroprevalence of and risk factors for toxoplasmosis in sheep from different properties in the Jaboticabal microregion, São Paulo State, Brazil were determined. Antibodies to Toxoplasma gondii were found in sera of 52.0% of 488 sheep tested by indirect fluorescent antibody test (IFAT >= 64). T gondii seropositivity in sheep was significantly associated with gender of the sheep, pasturing system, contact with cats, and the use of mineral supplements and the type of feed. (C) 2009 Elsevier Ltd. All rights reserved.

Piscinoodinium pillulare (Schäperclaus, 1954) Lom, 1981 (Dinoflagellida) infection in cultivated freshwater fish from the Northeast region of São Paulo State, Brazil: parasitological and pathological aspects

O Centro de Aqüicultura, Unesp, Jaboticabal, SP, Brasil, recebeu peixes para diagnose, os quais apresentavam aglomeração nas bordas dos viveiros e na entrada da água. Dos 194 casos diagnosticados, 53 apresentavam estruturas brancas circulares ou ovais, imóveis, medindo 162 mm de diâmetro, identificadas como o dinoflagelado Piscinoodinium pillulare. em 34 casos, os parasitos estavam presentes nas brânquias, em 2 casos, no corpo e em 9 casos, em ambos. Dos 53 casos observados, 31 eram o híbrido tambacu; 7, o Piaractus mesopotamicus; 6, o Colossoma macropomum; 5, o Leporinus macrocephalus; 3, o Oreochromis niloticus; e 1, o Prochilodus lineatus. Os peixes apresentaram aumento da produção de muco no corpo e nas brânquias e equimoses no pedúnculo caudal e nos opérculos. As brânquias também apresentaram palidez, congestão e petéquias. A histopatologia revelou a presença de grande número de trofontes situados entre as lamelas secundárias, fixados ou não ao epitélio. As lamelas primárias mostraram hemorragias intersticiais, severa hiperplasia do epitélio e das células caliciformes e infiltrado inflamatório. O presente trabalho é o primeiro relato de P. pillulare no Brasil e enfatiza a importância dos dinoflagelados, que causaram significativas perdas econômicas entre 1995 e 1997.

Occurrence of Theileria equi in horses raised in the Jaboticabal microregion, São Paulo State, Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Frequency of Blastocystis hominis and other intestinal parasites in stool samples examined at the Parasitology Laboratory of the School of Pharmaceutical Sciences at the São Paulo State University, Araraquara

Blastocystis hominis é um protozoário, causador de infecção intestinal denominada blastocistose humana, cujo diagnóstico é realizado pelo exame coproparasitológico e por meio de técnicas de coloração permanente. Este estudo foi desenvolvido para avaliar a freqüência da infecção por Blastocystis hominis em habitantes da região de Araraquara/SP, bem como comparar diferentes métodos para a pesquisa desse protozoário em amostras de fezes. Foram estudadas 503 amostras de fezes submetidas ao exame direto a fresco, às técnicas de Faust e cols, Lutz e de Rugai e cols, além das colorações pela hematoxilina férrica, tricrômio e de Kinyoun modificada. Entre as 503 amostras examinadas, 174 (34,6%) apresentaram-se positivas para a presença de parasitas intestinais. O protozoário e o helminto mais freqüentes foram Entamoeba coli (14,6%) e Strongyloides stercoralis (6,7%), respectivamente. Blastocystis hominis foi observado em 23 (4,6%) amostras fecais com consistência predominantemente pastosa, não caracterizando quadro diarréico. Apesar da baixa freqüência de Blastocystis hominis encontrada na região de Araraquara, comparativamente a outras regiões brasileiras, é importante a realização do diagnóstico laboratorial desse protozoário. O encontro de Blastocystis hominis em material fecal é indicativo de contaminação de alimentos e água de consumo, desde que se admita a rota de transmissão oral-fecal desse parasita, o que implica na orientação da população sobre as medidas de saneamento básico e higiene como meio para se controlar problemas de saúde ocasionados pelos enteroparasitas.

Organochlorine pesticides and polychlorinated biphenyls in soil and water samples in the northeastern part of São Paulo State, Brazil

Detailed analyses of persistent organic pollutants (POPs) such as organochlorine pesticides (OCPs), hexachlorocyclohexane (HCH) isomers (HCHs), dichlorodiphenyltrichloro ethane (DDT) and its metabolites (DDTs) and congeners of polychlorinated biphenyls (PCBs) in soil and surface water from the northeastern São Paulo, Brazil allowed the evaluation of the contamination status, distribution and possible pollution sources. The pesticides and PCBs demonstrated markedly different distributions, reflecting different agricultural, domestic and industrial usage in each region studied. The ranges of HCH, DDT, and PCBs concentrations in the soil samples were 0.05-0.92, 0.12-11.01, 0.02-0.25 ng g(-1) dry wt, respectively, and in the surface water samples were 0.02-0.6, 0.02-0.58 and 0.02-0.5 ng l(-1), respectively. Overall elevated levels of DDT and PCB were recorded in region 2, a site very close to melting, automotive batteries industries, and agricultural practice regions. High ratios of metabolites of DDT to DDT isomers revealed the recent use of DDT in this environment. The sources of contamination are closely related to human activities, such as domestic and industrial discharge, street runoff, agricultural pesticides and soil erosion, due to deforestation as well as atmospheric transport. (c) 2006 Elsevier Ltd. All rights reserved.

Ecological aspects of hermit crabs (Crustacea, Anomura, Paguroidea) off the northern coast of São Paulo State, Brazil

The occurrence of species of hermit crabs and their ecological distribution in soft bottoms off Ubatuba, São Paulo, Brazil were analyzed. To better understand the distribution of the species in relation to environmental factors, the similarity and species-diversity indexes were calculated. Paguroideans were sampled monthly from January through December 2000. The trawls were made with two otter-trawl nets at 13 different sites, at depths of 2-40 m. Water temperature, salinity, sediment texture, and organic matter content were measured. Gastropod shells occupied by hermit crabs were also assessed. A total of 1,238 specimens was collected, belonging to the families Diogenidae and Paguridae, comprising seven genera and thirteen species. The most abundant hermit crab species were Dardanus insignis (761 specimens) and Loxopagurus loxochelis (351 specimens). Phimochirus holthuisi is newly reported from the São Paulo coast. The highest diversity index was found for the shallower sites near rocky shores. The results of the grouping analysis for sites and species indicated three distinct groups for sites, and four groups for species. This suggests that the occurrence of these anomurans is associated with the environmental and biotic factors analyzed.

Ecological distribution and reproductive period of the hermit crab Loxopagurus loxochelis (Anomura, Diogenidae) on the northern coast of São Paulo State, Brazil

The present study aimed to determine the ecological distribution of Loxopagurus loxochelis as a function of selected environmental factors, as well as its reproductive period based on the combined analysis of the presence of ovigerous females and the development of the gonad. The collections were carried out monthly from January to December 2000 in the region of Ubatuba (SP), using a fishing boat equipped with two double rig nets, in isobaths of 5, 10, 15, 20, 25, 30, 35 and 40 m, at which depths samples of sediment and water were collected. The cephalothoracic shield length and sex of the animals were determined; the abdomen was dissected to verify gonad development stages. A total of 334 individuals was obtained ( 196 males, 48 ovigerous females and 90 non-ovigerous females) with sizes varying from 3.0 to 8.6 mm (5.7 +/- 1.0 mm). A greater abundance of L. loxochelis (95.2%) was observed at depths of 20 and 25 m. These sites mainly revealed a substratum stable with a very fine sand fraction, which facilitates the habit of embedding shown by this hermit. With regard to gonadal analysis, it was possible to classify four gonad development stages for each sex: immature, rudimentary, developing and developed. It was observed that in the winter months about 71% of the females had gonads either developing or developed and 67% were ovigerous. Therefore, the winter period can be considered the peak of reproduction for this species, characterizing a typical seasonal-continuous reproduction.

Reproductive pattern of the South American endemic shrimp Artemesia longinaris (Decapoda : Penaeoidea), off São Paulo State, Brazil

Sexual maturity, temporal reproductive pattern, and recruitment of juveniles were examined for the penaeoid shrimp Artemesia longinaris sampled for five and a half years in a tropical locality off the coast of São Paulo (23 degrees S), Brazil. Monthly samples were taken from January 1998 to June 2003 at depths between 5 and 45 m. Ovarian maturity was used to examine breeding in adult females. Recruitment was defined as the percentage of juveniles of the total number of individuals in each month and season. A total of 10 288 females and 5 551 males were collected. Estimated sizes (carapace length) at the onset of sexual maturity were 11.0 mm and 13.4 mm for males and females, respectively. Over the five and a half years, females with ripe gonads were found in every season, with the highest percentages in summer (January-March). Juvenile shrimps occur-red year-round. These results suggest a continuous reproduction of A. longinaris with temperature acting as an environmental stimulus for the duration of the ovary development cycle. These data and the hypothesis of the intrusion of the South Atlantic Central Water mass, which lowered water temperature and raised plankton production, suggest that the end of spring and the beginning of summer were the principal reproductive months. The classical paradigm of continuous reproduction at lower latitudes, with increased seasonality of breeding period at higher latitudes seems to apply to this species.

Abundance and ecologic distribution of the shrimp Rimapenaeus constrictus (Crustacea : Penaeidae) on the northern coast of São Paulo State, Brazil

The abundance and ecologic distribution of the shrimp R. constrictus were compared among three different embayments within the northern coast of São Paulo State (23degreesS, 45degreesW); i.e. Mar Virado (MV), Ubatuba (UBA) and Ubatumirim (UBM). Key environmental factors were monitored for a better understanding of the distributional patterns of this species, namely temperature, salinity, depth, organic matter content and texture of sediments. In each bay, six transects were delimited, four parallel to the coastline and the other two in areas adjacent to rocky shores. Monthly samples were taken over a 2-year period (1998 and 1999), using a shrimp fishing boat equipped with double-rig nets. Abundance data were treated separately according to environmental characteristics. A total of 4978 specimens was obtained; 921 at MV, 1948 at UBA and 2109 at UBM. The spatial distribution of R. constrictus differed among bays. Higher abundance values were recorded at areas where silt and clay comprised less than 70% of the sediment. A more diversified sediment at UBM and UBA apparently favours the establishment of this species in the region. Its abundance also followed a seasonal trend, higher during spring and summer when intrusions of cold South Atlantic Coastal Waters (SACW) are frequent, promoting the migration of this shrimp to more sheltered areas. These results suggest that sediment type and temperature are the most important variables affecting the spatial and seasonal distribution of this species.

Sexual maturity of the speckled swimming crab Arenaeus cribrarius (Lamarck, 1818) (Decapoda, Brachyura, Portunidae), in the Ubatuba Littoral, São Paulo state, Brazil

The sizes at morphological and physiological maturity of male and female Arenaeus cribrarius were estimated to determine if both events are synchronous. Animals were captured with otto-trawls at Ubatuba, Brazil. A total of 2356 specimens, 977 males and 1379 females, were obtained. The major carapace width without spines (CW), the propodus length of the major cheliped (PL) and the width of the 5th abdominal somite (AW) were measured with vernier calipers. Allometric relationships and gonadal development were analyzed to determine the maturity in both sexes. The size at the onset of male morphological maturity was estimated at CW 52 mm, smaller than the CW 63.4 mm physiological maturity size observed. For females, these events are synchronous since both estimates converged at CW 59.7 mm. The onset of functional sexual maturity in A. cribrarius at CW 63.4 and 59.7 mm in males and females, respectively, would indicate a minimum size of CW 64 mm for fishing purposes. Differences between allometric and gonadal estimates indicate the importance of considering both methods. A comparison of the present results with other available data in portunid crabs is provided.

Reproduction of Oligosarcus hepsetus (Cuvier, 1829) (Characiforms) in the Serra do Mar State Park, São Paulo, Brazil

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)